If you want to define hot rectangles in a window, you specify their location and size like this:

Code:
<If MouseIsOverWindowRect  WINDOW_NAME X_POS Y_POS WIDTH HEIGHT>
The numbers refer to the client area of the window that you click manually.

Alternatively, if you want to define a hot rectangle relative to the screen as a whole, you write this:

Code:
<If MouseIsOverScreenRect  X_POS Y_POS WIDTH HEIGHT>
In this case the numbers refer to the screen, not any particular window.

Modifiers aren't a problem with WoW although there may not be a convenient syntax for using them, depending on what you want to do. Shift states used to be a problem with WoW but I think (I hope) that they are fixed in the current test build.